In order to explore the function and efficiency of emergy input-output of Hunan’s agro-ecosystem, and reveal the regional interrelationship among human, natural resources and environment, the author adopted emergy theory as the research method, and did empirical analysis on the emergy structure, function and efficiency of Hunan’s agro-ecosystem by utilizing the input-output data of Hunan agriculture in 2009. The results showed that: (1) Hunan agriculture had characteristics of traditional agricultural production, depended comparatively highly on the labor force and animal power. The contribution of chemical fertilizer on the system was the highest in industrial auxiliary emergy, and the agricultural mechanization level was still low. The proportion of renewable industrial auxiliary energy was also low, so the development potential and prospects of agricultural green energy were comparatively large. The products obtained low prices, which not only neglected the contribution of natural resources and environment, but also reflected the characteristics of short industrial chain and low added value of Hunan agriculture. The emergy output of planting industry and animal industry owned dominated proportion in the agro-ecosystem, while the product prices were lower than those of forestry industry and fishery industry. (2) The results showed characteristics of the system’s function. Though the system did not own a high environmental loading ratio, its carrying capacity of population was overloading. The system’s sustainable development index was 5.96 which not only showed its vitality and development potential, but also showed the undeveloped economy and not high pressure of natural resources and environment. (3) The results also showed characteristics of the system’s efficiency. The emergy input-output of system was slightly lower than the national level in 2009, which showed relatively apparent extensive development characteristics. Therefore, it’s necessary to control the rapid population growth, transfer the rural surplus labor force, further adjust the agricultural structure and product structure, strengthen the development and utilization of agricultural technology, extend the industrial chain and enhance the agricultural mechanization and modernization level, which were the basic policy directions of Hunan Province.